I was one of the biggest skeptics, but now I'm >95% certain they're intimate. Like everyone else said, he "went there" at the end.
The serialization has been too subtle with the way it's ended chapters after they get a little bit intimate, probably due to censorship regulations for weekly manga, so it was extremely ambiguous how far they'd gone. Thankfully, the volumes have less constrained expression.
I mean, obviously if they were a "real" married couple, it never would've been ambiguous whether they were having sex. But common sense doesn't always apply to notoriously slow-paced Japanese youth romances. In any case... yeah, good for them. 🙂